Re: [Bioc-devel] Updating Package Issue

[Kern, Lori via Bioc-devel]

What is the name of your package?

Please keep in mind there are always two active branches of Bioconductor, 
currently RELEASE_3_18 and devel.  Based on the information provided   1.28.0 
would refer to a release version of a package while a verison number of 1.29.0 
would indicate a devel version of the package.






Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Tallulah 
Andrews 
Sent: Tuesday, April 2, 2024 11:14 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Updating Package Issue

Last week I updated my package to fix a build error and pushed the devel
branch back to bioconductor, which I confirmed by cloning the devel branch
on a different computer and I see my changes there. However, the
multiplatform build is still using the wrong version (1.28, vs my corrected
version 1.29), thus getting the build error.

How do I get the multiplatform build to use my updated version?

Cheers,
Tallulah Andrews

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Re: [Bioc-devel] updating package on the development version

[Shepherd, Lori]

Please see this post indicating that we are having trouble with our website and 
are in process of fixing it.  We have located the issue and pushed a fix and 
once applied the landing pages should generate properly.

https://stat.ethz.ch/pipermail/bioc-devel/2020-June/016923.html


Please check the build reports for the version numbers that are being used to 
build the package.

http://bioconductor.org/checkResults/

Keeping in mind there can be up to a 48 hour delay to see the results as 
described here:

http://bioconductor.org/developers/how-to/troubleshoot-build-report/

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Dwivedi, 
Bhakti 
Sent: Thursday, June 18, 2020 4:24 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] updating package on the development version

Hi,

I am trying to update previous release of my package (GISPA) on the development 
version.

I pushed the changes and new release GISPA 1.13.1 following 
https://secure-web.cisco.com/16G6QGHF8mpcsjsZBAAOMWj_a4_z0hmCZlj_TnB4TkGbw3lcmQkHHEjOqoyzLjoOMRn1aXjkTjb5avdzEYK8TvzOinzWcd9qWMiZtKViQYb59qlnna0b2zm1kpo9g5N-CAfehjdWj1aJjXXzU0Hr8DFvi9egMpJ8mJfKVtjZIxiNHpmVpAVpylYQTaAhqJ00j8m4g_-g32S9NI3JBhD0t4AqG-FOe6_XBx_MtqxawqmeCbMmzb7ACMy2fDyMtMWJN_8CFfp0MxJHYuURFn_zJFFrA_8OC5MS263jFlJ4tkGIjjP4i3l23Pk98aN0pleohwwTq6H5r4yXwIUIJZ1UtYixHkMKeMzfgh7Mx2jvPXCs/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F

But, I do not see the change on the bioconductor development version 
http://secure-web.cisco.com/1BfCJ7lm3FxR9215Gg0wJ4F_f-OUbGZlfSX7Ht1DBVyLt-CZZV-KC00A6xzrjCgeuhtuBWXSLpVmnjtVS2OXstGp5uPIT9ZrzhInLClCHaban0Vu4Cgjcat6pKhyv0_mkXT3BDemwUsYEc-n5Ci7Hg5ZyWVJNiFi8RXqmJZ7jivCEJbsbmPLkns3Aqlvm7sIpUsbyrHU_3sZB9ThrXyRAg1i6MYujiums1jeOJyKkH8xJ8rzlg4SZosumRATLEpNxRcqx0vJYGendXkAFaOLdducAMIKK1cFguQP3GuBIZGWXXTBajVSvf3AtXUEkgCGHMX_okMSo4UDIdulKBzh1bxvq1SjHw4IhYlMYjTUg9KI/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FGISPA.html.
 Where can I view the changes and make sure it passed all the checks?

Regards,
Bhakti





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Re: [Bioc-devel] Updating package via git fails

[Spivakov, Mikhail]

Sorry have realised I cloned with https!

Many apologies.

Mikhail

From: "Spivakov, Mikhail" 
Date: Thursday, 24 October 2019 at 17:01
To: "bioc-devel@r-project.org" 
Subject: Updating package via git fails

Hello!

I’ve just made some changes to our Chicago package that help avoid some common 
errors our users have encountered due to mis-specified parameters.

I tried pushing the update to github (push origin master), but it fails with 
“fatal: remote error: FATAL: W any packages/Chicago nobody DENIED by fallthru”.

I have got the username set and the public key uploaded. Could you please 
advise if there is any other obvious reason why this could fail?

Thanks so much,
Mikhail


--
Mikhail Spivakov, PhD
Group Leader and Senior Lecturer (Assoc. Professor)
MRC London Institute of Medical Sciences
Imperial College Faculty of Medicine
Hammersmith Hospital Campus
London W12 0NN


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Re: [Bioc-devel] updating package

[Turaga, Nitesh]

Hi,

It seems like the email is configured correctly on BiocCredentials app. It is 
because the account is not activated it doesn't work. You'd have to first 
activate your account before moving forward with setting a password.

I've added your GitHub credentials to the account. 

Best,

Nitesh 

> On Jun 14, 2019, at 11:01 AM, ostro...@mskcc.org wrote:
> 
> 
> Hi,
> I'd like to update my package Clonality 
> https://bioconductor.org/packages/release/bioc/html/Clonality.html
> I used to do it through svn but as I understand it's not possible now.
> 
> I can't connect it to my git page with updated package 
> https://github.com/IOstrovnaya/Clonality
> 
> When I enter my email  ostro...@mskcc.org here  
> https://git.bioconductor.org/BiocCredentials/account_activation/ I can't 
> login and resetting the password doesn't work.
> 
> Can you please help me establish my account on bioconductor and connect it to 
> my github?
> 
> Thank you!!!
> Irina
> 
> =
> 
> Please note that this e-mail and any files transmitted from
> Memorial Sloan Kettering Cancer Center may be privileged, confidential,
> and protected from disclosure under applicable law. If the reader of
> this message is not the intended recipient, or an employee or agent
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Re: [Bioc-devel] Updating package development version

[Hervé Pagès]

Hi Pedro,

The build system didn't pick up your changes because of an issue with
the script that we use to propagate the latest package changes to the
build machines. Sorry for that. The issue should be fixed now so
hopefully you'll see CEMiTool 0.99.9 on tomorrow's build report
(the report is updated every day):

  https://bioconductor.org/checkResults/3.6/bioc-LATEST/

and also on the package landing page:

  https://bioconductor.org/packages/CEMiTool

Don't hesitate to let us know if things don't look right.

Thanks,
H.

On 08/18/2017 11:53 AM, James W. MacDonald wrote:

On Fri, Aug 18, 2017 at 1:46 PM, Pedro Russo  wrote:


Dear maintainers,

I've followed the tutorials for updating my package CEMiTool in the new Git
server as detailed in:

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_developers_how-2Dto_git_bug-2Dfix-2D=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=H1WAQWYzwpfHNOWFNW3wGMBTMN4fLZ4Tql6ogaqwOlM=eUQYB_e3j9xcXHLEmJIArJXKQvOTfcgOeiaOWBudE-k=
in-release-and-devel/

including the steps

git checkout master
git push upstream master
git push origin master

However, when I execute useDevel() and biocLite("CEMiTool"), I see that the
changes I made aren't there.



When did you make those changes? Do note that it takes a day or so for any
changes to propagate through the build servers, so changes don't appear
right away.





The url for my package,
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_devel_bioc_html_CEMiTool.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=H1WAQWYzwpfHNOWFNW3wGMBTMN4fLZ4Tql6ogaqwOlM=N2Jy5WDi8yLdiiDOuCVl9p3aLAxxW4wjBjipOuAyn6s=

also shows a previous version of the package.

I'm new to Bioconductor package maintenance, so I apologize if I'm missing
anything simple, but I'm really stuck!

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Program in Computational Biology
Division of Public Health Sciences
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P.O. Box 19024
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E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] Updating package

[Martin Morgan]

On 01/05/2017 01:25 PM, Charles Determan wrote:

I committed my changes earlier this morning from the 'devel' branch via
the 'git svn dcommit --add-author-from' the website
(https://www.bioconductor.org/developers/how-to/git-mirrors/).  I have
yet to see any changes on the build page though for the `devel`
(http://master.bioconductor.org/checkResults/3.5/bioc-LATEST/).  Did I
miss another step or is the build process reporting slow or perhaps I am
looking in the wrong place still?


builds run nightly, check at the top of the page 
http://master.bioconductor.org/checkResults/3.5/bioc-LATEST/ for the 
date of the svn 'snapshot' and the date the build report is published. 
Currently these are


Snapshot Date: 2017-01-03 17:15:43 -0500 (Tue, 03 Jan 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks
Last Changed Rev: 125601 / Revision: 125601
Last Changed Date: 2017-01-03 17:11:11 -0500 (Tue, 03 Jan 2017)

This page was generated on 2017-01-04 16:34:16 -0500 (Wed, 04 Jan 2017).

You can see here

https://github.com/Bioconductor-mirror/OmicsMarkeR

that your commit is reflected in the mirror of the svn repository, and with

  svn co 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR

  cd OmicsMarkeR
  svn log|head

with output

OmicsMarkeR$   svn log|head

r125696 | c.determan | 2017-01-05 10:31:07 -0500 (Thu, 05 Jan 2017) | 3 
lines


increment sub-sub version for bug fix

From: Charles Determan 

r123124 | hpa...@fhcrc.org | 2016-10-27 18:00:06 -0400 (Thu, 27 Oct 
2016) | 1 line


auxiliary -concordance.tex files don't belong to the package source tree

that your commit has made it to the definitive location, the svn 
repository for your package.


Martin





Regards,
Charles

On Thu, Jan 5, 2017 at 9:47 AM, Charles Determan > wrote:

That seems to have been the issue.  It had been some time since I
needed to commit to bioconductor I forgot my username was
different.  Thank you Martin for pointing that simple problem out.
I have now 'dcommit' my 'devel' branch so if I understand correctly
the changes should be with bioconductor to apply accordingly.

Regards,
Charles

On Thu, Jan 5, 2017 at 9:22 AM, Martin Morgan
> wrote:

On 01/05/2017 10:18 AM, Charles Determan wrote:

Not to be pushy but did anyone have any insights with this?
I would hate
to have my package still sitting with the bug fix it requires.


maybe svn credentials,

 git svn rebase --username=c.determan

??


Thanks,
Charles

On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan
>
wrote:

Hi,

I received a notification that my package was failing
some tests.  I have
since made the necessary fixes and pushed my changes to
the github repo.
Previously this would result in http://gitsvn.bioconductor.
org/git-push-hook updating the package for
bioconductor.  I noticed
however that this delivery fails and that the git-svn
bridge is no longer
available.

How should I modify my current repository to update my
package
accordingly?

I have my local changes in the 'devel' branch.
I ran the update_ remotes.sh
I run 'git svn rebase' but I get the following error:

Can't create session: Unable to connect to a repository
at URL '

https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR

':
Unexpected server error 500 'Internal Server Error' on
'/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at
/mingw64/share/perl5/site_perl/Git/SVN.pm line 717.

What did I miss here?
Thanks,

Charles


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Re: [Bioc-devel] Updating package

[Charles Determan]

That seems to have been the issue.  It had been some time since I needed to
commit to bioconductor I forgot my username was different.  Thank you
Martin for pointing that simple problem out.  I have now 'dcommit' my
'devel' branch so if I understand correctly the changes should be with
bioconductor to apply accordingly.

Regards,
Charles

On Thu, Jan 5, 2017 at 9:22 AM, Martin Morgan  wrote:

> On 01/05/2017 10:18 AM, Charles Determan wrote:
>
>> Not to be pushy but did anyone have any insights with this?  I would hate
>> to have my package still sitting with the bug fix it requires.
>>
>
> maybe svn credentials,
>
>  git svn rebase --username=c.determan
>
> ??
>
>
>> Thanks,
>> Charles
>>
>> On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan 
>> wrote:
>>
>> Hi,
>>>
>>> I received a notification that my package was failing some tests.  I have
>>> since made the necessary fixes and pushed my changes to the github repo.
>>> Previously this would result in http://gitsvn.bioconductor.
>>> org/git-push-hook updating the package for bioconductor.  I noticed
>>> however that this delivery fails and that the git-svn bridge is no longer
>>> available.
>>>
>>> How should I modify my current repository to update my package
>>> accordingly?
>>>
>>> I have my local changes in the 'devel' branch.
>>> I ran the update_ remotes.sh
>>> I run 'git svn rebase' but I get the following error:
>>>
>>> Can't create session: Unable to connect to a repository at URL '
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR
>>> ':
>>> Unexpected server error 500 'Internal Server Error' on
>>> '/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at
>>> /mingw64/share/perl5/site_perl/Git/SVN.pm line 717.
>>>
>>> What did I miss here?
>>> Thanks,
>>>
>>> Charles
>>>
>>>
>> [[alternative HTML version deleted]]
>>
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>>
>>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
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> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
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>

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Re: [Bioc-devel] Updating package

[Martin Morgan]

On 01/05/2017 10:18 AM, Charles Determan wrote:

Not to be pushy but did anyone have any insights with this?  I would hate
to have my package still sitting with the bug fix it requires.


maybe svn credentials,

 git svn rebase --username=c.determan

??



Thanks,
Charles

On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan 
wrote:


Hi,

I received a notification that my package was failing some tests.  I have
since made the necessary fixes and pushed my changes to the github repo.
Previously this would result in http://gitsvn.bioconductor.
org/git-push-hook updating the package for bioconductor.  I noticed
however that this delivery fails and that the git-svn bridge is no longer
available.

How should I modify my current repository to update my package
accordingly?

I have my local changes in the 'devel' branch.
I ran the update_ remotes.sh
I run 'git svn rebase' but I get the following error:

Can't create session: Unable to connect to a repository at URL '
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR':
Unexpected server error 500 'Internal Server Error' on
'/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at
/mingw64/share/perl5/site_perl/Git/SVN.pm line 717.

What did I miss here?
Thanks,

Charles



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Re: [Bioc-devel] Updating package

[Charles Determan]

Not to be pushy but did anyone have any insights with this?  I would hate
to have my package still sitting with the bug fix it requires.

Thanks,
Charles

On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan 
wrote:

> Hi,
>
> I received a notification that my package was failing some tests.  I have
> since made the necessary fixes and pushed my changes to the github repo.
> Previously this would result in http://gitsvn.bioconductor.
> org/git-push-hook updating the package for bioconductor.  I noticed
> however that this delivery fails and that the git-svn bridge is no longer
> available.
>
> How should I modify my current repository to update my package
> accordingly?
>
> I have my local changes in the 'devel' branch.
> I ran the update_ remotes.sh
> I run 'git svn rebase' but I get the following error:
>
> Can't create session: Unable to connect to a repository at URL '
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR':
> Unexpected server error 500 'Internal Server Error' on
> '/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at
> /mingw64/share/perl5/site_perl/Git/SVN.pm line 717.
>
> What did I miss here?
> Thanks,
>
> Charles
>

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